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Hideki Kandori - One of the best experts on this subject based on the ideXlab platform.

  • Properties of the Anion-Binding Site of pharaonis Halorhodopsin Studied by Ultrafast Pump−Probe Spectroscopy and Low-Temperature FTIR Spectroscopy
    Journal of Physical Chemistry B, 2009
    Co-Authors: Keisuke Nakashima, Mikihiro Shibata, Takumi Nakamura, Tahei Tahara, Satoshi Takeuchi, Makoto Demura, Hideki Kandori
    Abstract:

    Halorhodopsin (HR) is a light-driven Chloride Pump. Cl− is bound in the Schiff base region of the retinal chromophore, and unidirectional Cl− transport is probably enforced by the specific hydrogen-bonding interaction with the protonated Schiff base and internal water molecules. It is known that HR from Natronobacterium pharaonis (pHR) also Pumps NO3− with similar efficiency, suggesting that NO3− binds to the Cl−-binding site. In the present study, we investigated the properties of the anion-binding site by means of ultrafast Pump−probe spectroscopy and low-temperature FTIR spectroscopy. The obtained data were surprisingly similar between pHR−NO3− and pHR−Cl−, even though the shapes and sizes of the two anions are quite different. Femtosecond Pump−probe spectroscopy showed very similar excited-state dynamics between pHR−NO3− and pHR−Cl−. Low-temperature FTIR spectroscopy of unlabeled and [ζ-15N]Lys-labeled pHR revealed almost identical hydrogen-bonding strengths of the protonated retinal Schiff base betwe...

  • properties of the anion binding site of pharaonis halorhodopsin studied by ultrafast Pump probe spectroscopy and low temperature ftir spectroscopy
    Journal of Physical Chemistry B, 2009
    Co-Authors: Keisuke Nakashima, Mikihiro Shibata, Takumi Nakamura, Tahei Tahara, Satoshi Takeuchi, Makoto Demura, Hideki Kandori
    Abstract:

    Halorhodopsin (HR) is a light-driven Chloride Pump. Cl− is bound in the Schiff base region of the retinal chromophore, and unidirectional Cl− transport is probably enforced by the specific hydrogen-bonding interaction with the protonated Schiff base and internal water molecules. It is known that HR from Natronobacterium pharaonis (pHR) also Pumps NO3− with similar efficiency, suggesting that NO3− binds to the Cl−-binding site. In the present study, we investigated the properties of the anion-binding site by means of ultrafast Pump−probe spectroscopy and low-temperature FTIR spectroscopy. The obtained data were surprisingly similar between pHR−NO3− and pHR−Cl−, even though the shapes and sizes of the two anions are quite different. Femtosecond Pump−probe spectroscopy showed very similar excited-state dynamics between pHR−NO3− and pHR−Cl−. Low-temperature FTIR spectroscopy of unlabeled and [ζ-15N]Lys-labeled pHR revealed almost identical hydrogen-bonding strengths of the protonated retinal Schiff base betwe...

  • Ultrafast Pump-probe study of the primary photoreaction process in pharaonis halorhodopsin: halide ion dependence and isomerization dynamics.
    Journal of Physical Chemistry B, 2008
    Co-Authors: Takumi Nakamura, Mikihiro Shibata, Hideki Kandori, Satoshi Takeuchi, Makoto Demura, Tahei Tahara
    Abstract:

    Halorhodopsin is a retinal protein that acts as a light-driven Chloride Pump in the Haloarchaeal cell membrane. A Chloride ion is bound near the retinal chromophore, and light-induced all-trans → 13-cis isomerization triggers the unidirectional Chloride ion Pump. We investigated the primary ultrafast dynamics of Natronomonas pharaonis halorhodopsin that contains Cl−, Br−, or I− (pHR-Cl−, pHR-Br−, or pHR-I−) using ultrafast Pump−probe spectroscopy with ∼30 fs time resolution. All of the temporal behaviors of the Sn ← S1 absorption, ground-state bleaching, K intermediate (13-cis form) absorption, and stimulated emission were observed. In agreement with previous reports, the primary process exhibited three dynamics. The first dynamics corresponds to the population branching process from the Franck−Condon (FC) region to the reactive (S1r) and nonreactive (S1nr) S1 states. With the improved time resolution, it was revealed that the time constant of this branching process (τ1) is as short as 50 fs. The second d...

  • deprotonation of glu234 during the photocycle of natronomonas pharaonis halorhodopsin
    Chemical Physics Letters, 2006
    Co-Authors: Mikihiro Shibata, Yuko Saito, Makoto Demura, Hideki Kandori
    Abstract:

    Halorhodopsin (HR) is a light-driven Chloride Pump in haloarchaea. Our previous low-temperature Fourier-transform infrared (FTIR) study of pharaonis HR reported that the Chloride binding site is destabilized in the L1 intermediate because of the changes in its polar environment. The present FTIR spectroscopy of the wild-type and mutant pharaonis HR revealed that Glu234 becomes deprotonated in the L2 intermediate. This suggests that appearance of a negative charge at the extracellular surface prevents a Chloride ion from translocation toward the extracellular side.

  • internal water molecules of the proton Pumping halorhodopsin in the presence of azide
    Journal of the American Chemical Society, 2006
    Co-Authors: N. Muneda, Mikihiro Shibata, Makoto Demura, Hideki Kandori
    Abstract:

    : In the FTIR study of rhodopsins, we have so far found that strongly hydrogen-bonded water molecules (O-D stretch at <2400 cm-1) are only present in the proteins exhibiting proton-Pumping activity. Halorhodopsin (HR) is a light-driven Chloride Pump in haloarchaea, which does not possess such water molecules. On the other hand, it is known that addition of azide converts HR into a proton Pump. Although the mechanism has not been understood, we observed strongly hydrogen-bonded water molecules in the azide-bound HR of Natronobacterium pharaonis (pHR). This finding is consistent with the previous results, implying that the presence of strongly hydrogen-bonded water molecules is requested for the proton-Pumping function of rhodopsins.

Mikihiro Shibata - One of the best experts on this subject based on the ideXlab platform.

  • Properties of the Anion-Binding Site of pharaonis Halorhodopsin Studied by Ultrafast Pump−Probe Spectroscopy and Low-Temperature FTIR Spectroscopy
    Journal of Physical Chemistry B, 2009
    Co-Authors: Keisuke Nakashima, Mikihiro Shibata, Takumi Nakamura, Tahei Tahara, Satoshi Takeuchi, Makoto Demura, Hideki Kandori
    Abstract:

    Halorhodopsin (HR) is a light-driven Chloride Pump. Cl− is bound in the Schiff base region of the retinal chromophore, and unidirectional Cl− transport is probably enforced by the specific hydrogen-bonding interaction with the protonated Schiff base and internal water molecules. It is known that HR from Natronobacterium pharaonis (pHR) also Pumps NO3− with similar efficiency, suggesting that NO3− binds to the Cl−-binding site. In the present study, we investigated the properties of the anion-binding site by means of ultrafast Pump−probe spectroscopy and low-temperature FTIR spectroscopy. The obtained data were surprisingly similar between pHR−NO3− and pHR−Cl−, even though the shapes and sizes of the two anions are quite different. Femtosecond Pump−probe spectroscopy showed very similar excited-state dynamics between pHR−NO3− and pHR−Cl−. Low-temperature FTIR spectroscopy of unlabeled and [ζ-15N]Lys-labeled pHR revealed almost identical hydrogen-bonding strengths of the protonated retinal Schiff base betwe...

  • properties of the anion binding site of pharaonis halorhodopsin studied by ultrafast Pump probe spectroscopy and low temperature ftir spectroscopy
    Journal of Physical Chemistry B, 2009
    Co-Authors: Keisuke Nakashima, Mikihiro Shibata, Takumi Nakamura, Tahei Tahara, Satoshi Takeuchi, Makoto Demura, Hideki Kandori
    Abstract:

    Halorhodopsin (HR) is a light-driven Chloride Pump. Cl− is bound in the Schiff base region of the retinal chromophore, and unidirectional Cl− transport is probably enforced by the specific hydrogen-bonding interaction with the protonated Schiff base and internal water molecules. It is known that HR from Natronobacterium pharaonis (pHR) also Pumps NO3− with similar efficiency, suggesting that NO3− binds to the Cl−-binding site. In the present study, we investigated the properties of the anion-binding site by means of ultrafast Pump−probe spectroscopy and low-temperature FTIR spectroscopy. The obtained data were surprisingly similar between pHR−NO3− and pHR−Cl−, even though the shapes and sizes of the two anions are quite different. Femtosecond Pump−probe spectroscopy showed very similar excited-state dynamics between pHR−NO3− and pHR−Cl−. Low-temperature FTIR spectroscopy of unlabeled and [ζ-15N]Lys-labeled pHR revealed almost identical hydrogen-bonding strengths of the protonated retinal Schiff base betwe...

  • Ultrafast Pump-probe study of the primary photoreaction process in pharaonis halorhodopsin: halide ion dependence and isomerization dynamics.
    Journal of Physical Chemistry B, 2008
    Co-Authors: Takumi Nakamura, Mikihiro Shibata, Hideki Kandori, Satoshi Takeuchi, Makoto Demura, Tahei Tahara
    Abstract:

    Halorhodopsin is a retinal protein that acts as a light-driven Chloride Pump in the Haloarchaeal cell membrane. A Chloride ion is bound near the retinal chromophore, and light-induced all-trans → 13-cis isomerization triggers the unidirectional Chloride ion Pump. We investigated the primary ultrafast dynamics of Natronomonas pharaonis halorhodopsin that contains Cl−, Br−, or I− (pHR-Cl−, pHR-Br−, or pHR-I−) using ultrafast Pump−probe spectroscopy with ∼30 fs time resolution. All of the temporal behaviors of the Sn ← S1 absorption, ground-state bleaching, K intermediate (13-cis form) absorption, and stimulated emission were observed. In agreement with previous reports, the primary process exhibited three dynamics. The first dynamics corresponds to the population branching process from the Franck−Condon (FC) region to the reactive (S1r) and nonreactive (S1nr) S1 states. With the improved time resolution, it was revealed that the time constant of this branching process (τ1) is as short as 50 fs. The second d...

  • deprotonation of glu234 during the photocycle of natronomonas pharaonis halorhodopsin
    Chemical Physics Letters, 2006
    Co-Authors: Mikihiro Shibata, Yuko Saito, Makoto Demura, Hideki Kandori
    Abstract:

    Halorhodopsin (HR) is a light-driven Chloride Pump in haloarchaea. Our previous low-temperature Fourier-transform infrared (FTIR) study of pharaonis HR reported that the Chloride binding site is destabilized in the L1 intermediate because of the changes in its polar environment. The present FTIR spectroscopy of the wild-type and mutant pharaonis HR revealed that Glu234 becomes deprotonated in the L2 intermediate. This suggests that appearance of a negative charge at the extracellular surface prevents a Chloride ion from translocation toward the extracellular side.

  • internal water molecules of the proton Pumping halorhodopsin in the presence of azide
    Journal of the American Chemical Society, 2006
    Co-Authors: N. Muneda, Mikihiro Shibata, Makoto Demura, Hideki Kandori
    Abstract:

    : In the FTIR study of rhodopsins, we have so far found that strongly hydrogen-bonded water molecules (O-D stretch at <2400 cm-1) are only present in the proteins exhibiting proton-Pumping activity. Halorhodopsin (HR) is a light-driven Chloride Pump in haloarchaea, which does not possess such water molecules. On the other hand, it is known that addition of azide converts HR into a proton Pump. Although the mechanism has not been understood, we observed strongly hydrogen-bonded water molecules in the azide-bound HR of Natronobacterium pharaonis (pHR). This finding is consistent with the previous results, implying that the presence of strongly hydrogen-bonded water molecules is requested for the proton-Pumping function of rhodopsins.

Makoto Demura - One of the best experts on this subject based on the ideXlab platform.

  • Effect of Chloride binding on the thermal trimer-monomer conversion of halorhodopsin in the solubilized system.
    Biochemistry, 2009
    Co-Authors: Takanori Sasaki, Masakatsu Kamiya, Keiichi Kawano, Tomoyasu Aizawa, Naoki Kamo, Takashi Kikukawa, Makoto Demura
    Abstract:

    Halorhodopsin from Natronomonas pharaonis (NpHR) acts an inward-directed, light-driven Chloride Pump and forms a homotrimer. To evaluate effect of trimeric assembly, that is, intermolecular interaction, on the control or modulation of light-driven Chloride Pumping activity of individual HRs, it is important to understand the thermal and Chloride sensitivity of trimer dissociation and the structural stability of HR. In this study, the thermal dissociation of NpHR trimer to monomer in a dodecyl β-d-maltoside-solubilized system was investigated, using size-exclusion chromatography and visible absorption. In the absence of Cl−, NpHR retained the trimer assembly at 25 °C but dissociated to the monomer with an increase in temperature to >40 °C. On the other hand, in the presence of Cl−, the trimer assembly was maintained at 40 °C. The dissociation of the trimer to the monomer after incubation at 40 °C, which was determined via size-exclusion chromatography, depended on the Cl− concentration and showed a sigmoid...

  • Properties of the Anion-Binding Site of pharaonis Halorhodopsin Studied by Ultrafast Pump−Probe Spectroscopy and Low-Temperature FTIR Spectroscopy
    Journal of Physical Chemistry B, 2009
    Co-Authors: Keisuke Nakashima, Mikihiro Shibata, Takumi Nakamura, Tahei Tahara, Satoshi Takeuchi, Makoto Demura, Hideki Kandori
    Abstract:

    Halorhodopsin (HR) is a light-driven Chloride Pump. Cl− is bound in the Schiff base region of the retinal chromophore, and unidirectional Cl− transport is probably enforced by the specific hydrogen-bonding interaction with the protonated Schiff base and internal water molecules. It is known that HR from Natronobacterium pharaonis (pHR) also Pumps NO3− with similar efficiency, suggesting that NO3− binds to the Cl−-binding site. In the present study, we investigated the properties of the anion-binding site by means of ultrafast Pump−probe spectroscopy and low-temperature FTIR spectroscopy. The obtained data were surprisingly similar between pHR−NO3− and pHR−Cl−, even though the shapes and sizes of the two anions are quite different. Femtosecond Pump−probe spectroscopy showed very similar excited-state dynamics between pHR−NO3− and pHR−Cl−. Low-temperature FTIR spectroscopy of unlabeled and [ζ-15N]Lys-labeled pHR revealed almost identical hydrogen-bonding strengths of the protonated retinal Schiff base betwe...

  • properties of the anion binding site of pharaonis halorhodopsin studied by ultrafast Pump probe spectroscopy and low temperature ftir spectroscopy
    Journal of Physical Chemistry B, 2009
    Co-Authors: Keisuke Nakashima, Mikihiro Shibata, Takumi Nakamura, Tahei Tahara, Satoshi Takeuchi, Makoto Demura, Hideki Kandori
    Abstract:

    Halorhodopsin (HR) is a light-driven Chloride Pump. Cl− is bound in the Schiff base region of the retinal chromophore, and unidirectional Cl− transport is probably enforced by the specific hydrogen-bonding interaction with the protonated Schiff base and internal water molecules. It is known that HR from Natronobacterium pharaonis (pHR) also Pumps NO3− with similar efficiency, suggesting that NO3− binds to the Cl−-binding site. In the present study, we investigated the properties of the anion-binding site by means of ultrafast Pump−probe spectroscopy and low-temperature FTIR spectroscopy. The obtained data were surprisingly similar between pHR−NO3− and pHR−Cl−, even though the shapes and sizes of the two anions are quite different. Femtosecond Pump−probe spectroscopy showed very similar excited-state dynamics between pHR−NO3− and pHR−Cl−. Low-temperature FTIR spectroscopy of unlabeled and [ζ-15N]Lys-labeled pHR revealed almost identical hydrogen-bonding strengths of the protonated retinal Schiff base betwe...

  • Role of Arg123 in light-driven anion Pump mechanisms of pharaonis halorhodopsin.
    Photochemistry and Photobiology, 2009
    Co-Authors: Megumi Kubo, Masakatsu Kamiya, Keiichi Kawano, Akiteru Seki, Tomoyasu Aizawa, Seiji Miyauchi, Naoki Kamo, Takashi Kikukawa, Makoto Demura
    Abstract:

    Halorhodopsin (HR) acts as a light-driven Chloride Pump which transports a Chloride ion from the extracellular (EC) to the cytoplasmic space during a photocycle reaction that includes some photointermediates initiated by illumination. To understand the Chloride uptake mechanisms, we focused on a basic residue Arg123 of HR from Natronomonas pharaonis (NpHR), which is the only basic residue located in the EC half ion channel. By the measurements of the visible absorption spectra in the dark and the light-induced inward current through the membrane, it was shown that the Chloride binding and transport ability of NpHR completely disappeared by the change of arginine to glutamine. From flashphotolysis analysis, the photocycle of R123Q differed from that of wildtype NpHR completely. The response of the R123H mutant depended on pH. These facts imply that the positive charge at position 123 is essential for Chloride binding in the ground state and for the Chloride uptake under illumination. On the basis of the molecular structures of HR and the anion-transportable mutants of bacteriorhodopsin, the effects of the positive charge and the conformational change of the Arg123 side chain as well as the Chloride-Pumping mechanism are discussed.

  • Ultrafast Pump-probe study of the primary photoreaction process in pharaonis halorhodopsin: halide ion dependence and isomerization dynamics.
    Journal of Physical Chemistry B, 2008
    Co-Authors: Takumi Nakamura, Mikihiro Shibata, Hideki Kandori, Satoshi Takeuchi, Makoto Demura, Tahei Tahara
    Abstract:

    Halorhodopsin is a retinal protein that acts as a light-driven Chloride Pump in the Haloarchaeal cell membrane. A Chloride ion is bound near the retinal chromophore, and light-induced all-trans → 13-cis isomerization triggers the unidirectional Chloride ion Pump. We investigated the primary ultrafast dynamics of Natronomonas pharaonis halorhodopsin that contains Cl−, Br−, or I− (pHR-Cl−, pHR-Br−, or pHR-I−) using ultrafast Pump−probe spectroscopy with ∼30 fs time resolution. All of the temporal behaviors of the Sn ← S1 absorption, ground-state bleaching, K intermediate (13-cis form) absorption, and stimulated emission were observed. In agreement with previous reports, the primary process exhibited three dynamics. The first dynamics corresponds to the population branching process from the Franck−Condon (FC) region to the reactive (S1r) and nonreactive (S1nr) S1 states. With the improved time resolution, it was revealed that the time constant of this branching process (τ1) is as short as 50 fs. The second d...

Dieter Oesterhelt - One of the best experts on this subject based on the ideXlab platform.

  • Picosecond events in the photochemical cycle of the light-driven Chloride-Pump halorhodopsin
    Biophysical Journal, 2009
    Co-Authors: Hans-joachim Polland, Wolfgang Zinth, M. A. Franz, Wolfgang Kaiser, Peter Hegemann, Dieter Oesterhelt
    Abstract:

    The early events in halorhodopsin after light excitation are studied with picosecond time resolution. Absorption and fluorescence measurements show that the electronically excited state of the incorporated retinal has a lifetime of 5 ps. Within that time a red-shifted photoproduct is formed that remains stable for at least 2 ns.

  • primary reaction dynamics of halorhodopsin observed by sub picosecond ir vibrational spectroscopy
    Chemical Physics, 2006
    Co-Authors: Frank Peters, Jörg Tittor, Dieter Oesterhelt, Johannes Herbst, Rolf Diller
    Abstract:

    Abstract The primary all- trans to 13- cis chromophore isomerization of the light driven Chloride Pump halorhodopsin has been studied by means of transient absorption spectroscopy in the visible and mid-infrared regime at a time resolution of better than 100 and 220 fs, respectively. The picosecond vibrational dynamics are dominated by two time constants, i.e., 2 and 7.7 ps in accordance with the biphasic decay of the retinal excited electronic state and electronic ground state formation with 1.5 and 6.6 ps. The transient vibrational spectra of the participating electronic states strongly suggest the existence of two distinct S 1 populations as a result of an early branching reaction. It is shown that the 13- cis product is formed with the fast time constant, whereas the all- trans educt state is repopulated via both time constants. Concomitant protein dynamics are indicated by spectral changes on a similar time scale in the amide region.

  • probing origins of molecular interactions stabilizing the membrane proteins halorhodopsin and bacteriorhodopsin
    Structure, 2005
    Co-Authors: David A Cisneros, Dieter Oesterhelt, Daniel J Muller
    Abstract:

    Single-molecule atomic force microscopy and spectroscopy were applied to detect molecular interactions stabilizing the structure of halorhodopsin (HR), a light-driven Chloride Pump from Halobacterium salinarum. Because of the high structural and sequence similarities between HR and bacteriorhodopsin, we compared their unfolding pathways and polypeptide regions that established structurally stable segments against unfolding. Unfolding pathways and structural segments stabilizing the proteins both exhibited a remarkably high similarity. This suggests that different amino acid compositions can establish structurally indistinguishable energetic barriers. These stabilizing domains rather result from comprehensive interactions of all amino acids within a structural region than from specific interactions. However, one additional unfolding barrier located within a short segment of helix E was detected for HR. This barrier correlated with a Pi-bulk interaction, which locally disrupts helix E and divides a structural stabilizing segment.

  • structure of the light driven Chloride Pump halorhodopsin at 1 8 a resolution
    Science, 2000
    Co-Authors: Michael Kolbe, Lars-oliver Essen, Huseyin Besir, Dieter Oesterhelt
    Abstract:

    Halorhodopsin, an archaeal rhodopsin ubiquitous in Haloarchaea, uses light energy to Pump Chloride through biological membranes. Halorhodopsin crystals were grown in a cubic lipidic phase, which allowed the x-ray structure determination of this anion Pump at 1.8 angstrom resolution. Halorhodopsin assembles to trimers around a central patch consisting of palmitic acid. Next to the protonated Schiff base between Lys 242 and the isomerizable retinal chromophore, a single Chloride ion occupies the transport site. Energetic calculations on Chloride binding reveal a combination of ion-ion and ion-dipole interactions for stabilizing the anion 18 angstroms below the membrane surface. Ion dragging across the protonated Schiff base explains why Chloride and proton translocation modes are mechanistically equivalent in archaeal rhodopsins.

  • the three dimensional structure of halorhodopsin to 5 a by electron crystallography a new unbending procedure for two dimensional crystals by using a global reference structure
    Proceedings of the National Academy of Sciences of the United States of America, 2000
    Co-Authors: Edmund R S Kunji, Susanne Von Gronau, Dieter Oesterhelt, Richard Henderson
    Abstract:

    Electron microscopy does not, in principle, require highly ordered crystals to determine a high-resolution structure. Nevertheless, crystals of any type help to constrain the molecules into a more limited range of orientations and positions, from which it is easier to carry out structure determination. We describe an improved procedure for determination of crystalline disorder, which we have applied to poorly ordered two-dimensional crystals of the Chloride Pump halorhodopsin from Halobacterium salinarum. The new image analysis procedure involves the use of a reference projection calculated from a global three-dimensional map to carry out the initial cross-correlation analysis. Coupled with a greater number of images taken with field emission gun microscopes, this has allowed us to calculate a three-dimensional structure for halorhodopsin, in which the seven transmembrane helices and certain molecular features, such as the β-ionone ring of retinal, are now resolved.

Colin J Akerman - One of the best experts on this subject based on the ideXlab platform.